Neuronal mitochondria regulate synaptic physiology and cellular survival, and disruption of their function or transport causes neurological disease. We present a fluorescence method to selectively image mitochondrial dynamics in the mouse nervous system, in both live mice and acute explants. We show that axon damage and recovery lead to early and sustained changes in anterograde and retrograde transport. In vivo imaging of mitochondria will be a useful tool to analyze this essential organelle.